1) For the most part, totally ignore what bodyparts you're working and just focus on the movements. As for how you should set up your program - however you want! You can have a day for pull and a day for push, a day for upper body and a day for lower body, or a day for upper push/lower push/upper pull/lower pull.
2) I dunno about you but if i had anything but water during a workout id puke it right back up again. Theres no benefit to taking it during a workout that i know of. If anything, you want as much blood in your muscles as possible rather than wasting it on digesting proteins.